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- PDB-9j7y: the complex structure of MPXV M1R and nanobody M1R-01 -

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Basic information

Entry
Database: PDB / ID: 9j7y
Titlethe complex structure of MPXV M1R and nanobody M1R-01
Components
  • Entry-fusion complex associated protein OPG095
  • nanobody M1R-01
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / MPXV / nanobody / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyVirion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane / membrane / Entry-fusion complex associated protein OPG095
Function and homology information
Biological speciesMonkeypox virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsGe, J.W. / Fan, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: the complex structure of MPXV M1R and nanobody M1R-01
Authors: Ge, J.W. / Fan, M.
History
DepositionAug 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Entry-fusion complex associated protein OPG095
H: nanobody M1R-01


Theoretical massNumber of molelcules
Total (without water)34,2432
Polymers34,2432
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-11 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.270, 61.270, 167.499
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Entry-fusion complex associated protein OPG095 / EFC-associated protein OPG095 / Protein L1


Mass: 20624.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG099, MPXVgp080
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: M1LBP0
#2: Antibody nanobody M1R-01


Mass: 13619.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1M ammonium acetate, 0.1M Bis-Tris, ph5.5, 17% w/v PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 6593 / % possible obs: 59.66 % / Redundancy: 8 % / CC1/2: 0.99 / Net I/σ(I): 10.65
Reflection shellResolution: 2.58→2.67 Å / Num. unique obs: 109 / CC1/2: 0.541

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→26.86 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 31.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 317 4.81 %
Rwork0.2256 --
obs0.228 6593 59.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 0 0 2238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.604
X-RAY DIFFRACTIONf_dihedral_angle_d6.825315
X-RAY DIFFRACTIONf_chiral_restr0.082354
X-RAY DIFFRACTIONf_plane_restr0.02403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.680.3509540.30781266X-RAY DIFFRACTION24
2.68-26.860.26282630.2165010X-RAY DIFFRACTION95

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